Expertise and equipments

Expertise and equipment
ABiMS offers its expertise in data analysis , software and database development to scientific teams in the framework of collaborative projects.

Its service offer is distributed in five activities:
– e-infrastructure: computing cluster, Galaxy, JBrowse/Apollo, RStudio, banks, storage and scientific software
– Bio-analysis: data analysis -omics (RNAseq, genomics, metagenomics, metabarcoding, etc.)
– Software engineering: design of websites, software and databases
– Training: RNASeq, phylogeny, Linux, R, Python, …
– Support: for the use of computing resources (software, data, etc.)
The ABiMS platform provides access to its computing and storage infrastructure (2500 CPUs, 2.5 Po, GPU servers, BDD, BigMem 1-2 TB RAM) as well as an offer of more than 500 software and reference databases, which are deployed jointly with the IFBcore platforms.
Request an account: https://my.sb-roscoff.fr/manager2/register

Training

The ABiMS platform offers training courses with a triple objective:
– To teach users to become familiar with the e-infrastructure components they will need to carry out the computing aspects of their scientific projects: the Linux operating system, the cluster execution environment,
– To help users to handle specific software: the Galaxy platform, the R programming language.
– To enable users to perform analyses of their data by training them in statistical analysis methods, RNA-seq, genome assembly and annotation, metabarcoding
ABiMS team members also organise training sessions adapted to specific communities (Metabolomics) or projects (summer schools, CNRS schools, AVISAN schools).

Developments / Main achievements

In order to provide the scientific community with tools for analysing genomic and transcriptomic data from the Phaexplorer “France Genomics” project, the ABiMS platform is deploying on its HPC infrastructure environments for data visualisation and annotation through user-friendly interfaces based on the GGA project: galaxy-genome-annotation.github.io. https://phaeoexplorer.sb-roscoff.fr/home/

Within the framework of the European ELIXIR project, in close collaboration with the Genoscope and the EBI, the ABiMS platform has developed and maintained a reference genomic database dedicated to the transcriptomes of marine species, METdb (http://metdb.sb-roscoff.fr/metdb/). This database brings together public datasets from the MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project, Keeling et al. 2014) collaborative project and complementary datasets from research projects at the Roscoff Marine Station and the Genoscope. A total of 494 RNA-seq datasets comprising 233 different genera and 27 phyla were integrated using standardised and reproducible assembly and annotation protocols.
Within the framework of the ODATIS Ocean Pole of the IR DATATERRA, the ABiMS platform hosts the CDS-IS-SBR (Centre de données et services in situ de la Station Biologique de Roscoff) which is responsible for the national RESOMAR-Pelagos database. This database, which comes from the Network of Marine Stations and Observatories, contains biodiversity data on the coastal pelagic ecosystem (including time series). The main objective of such a database is to use the biological information acquired to answer scientific questions (e.g. the study of factors controlling the distribution and abundance of pelagic organisms at different spatial and temporal scales).

last update February 2022